<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-0873">
    <admin>
        <current_status>
            <date>2024-11-13</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-11-19</deposition>
            <header_release>2020-04-29</header_release>
            <map_release>2020-04-29</map_release>
            <update>2024-11-13</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Natural Science Foundation of China</funding_body>
                <code>31870835</code>
                <country>China</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-ATP state</title>
        <authors_list>
            <author>He Y</author>
            <author>Xu J</author>
        </authors_list>
        <keywords>P-type ATPase, lipid flippase, LIPID TRANSPORT</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">He Y</author>
                    <author order="2">Xu J</author>
                    <author order="3">Wu X</author>
                    <author order="4">Li L</author>
                    <title>Structures of a P4-ATPase lipid flippase in lipid bilayers.</title>
                    <journal_abbreviation>Protein Cell</journal_abbreviation>
                    <country>CN</country>
                    <volume>11</volume>
                    <first_page>458</first_page>
                    <last_page>463</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32303992</external_references>
                    <external_references type="DOI">doi:10.1007/s13238-020-00712-y</external_references>
                    <external_references type="ISSN">1674-8018</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6lcr</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Heterodimer of Dnf1-Cdc50</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Heterodimer of Dnf1-Cdc50</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="759272">Chaetomium thermophilum var. thermophilum DSM 1495</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Phospholipid-transporting ATPase</name>
                <natural_source database="NCBI">
                    <organism ncbi="759272">Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)</organism>
                    <strain>DSM 1495 / CBS 144.50 / IMI 039719</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.17537953099999998</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MAPPQEEGGGNGTELSMQRSRWATRRLTVKSGARKRLSLMTRAQAKNSATEKRQSGVTDDGSPAADGDQKEGSISSSNNG
GSAPRKLYFNLPLPPELKDEEGHPIQQFPRNKIRTAKYTPLSFIPKNLWFQFHNIANIFFLFLVILVIFPIFGGVNPGLN
SVPLIVIITVTAIKDAIEDYRRTILDIELNNAPVHRLQGWENVNVEKDNVSLWRRFKKANSRFFGSIWHLIERLWKEDAQ
SMRQRFASADPRMSIETRTAPWDPSHRRSVASHTEEIQMTPVPSPVPHDPDVPTVSSAIENEATLLQNLKGDLINHEIPV
SGKARFHKDAWKNLVVGDFVRIYNDDELPADIIILATSDPDGACYVETKNLDGETNLKVRQALRCGRTLKHARDCERAQF
VIESEPPQPNLYKYNGAIRWKQRVPWDPHGEPREMSEPIGIDNLLLRGCHLRNTEWALGVVVFTGHDTKIMMNAGITPSK
RARIARELNFNVICNFGILLIMCLIAAIANGIAWGKTDASLAWFEYGSIGGTPALTGFITFWAAVIVFQNLVPISLYISL
EIVRTLQAFFIYSDVGMYYEKIDQPCIPKSWNISDDVGQIEYIFSDKTGTLTQNVMEFKKATINGQPYGEAYTEAQAGMD
RRRGINVEEEAKVIREEIAAAKVRAIRGLRELHDNPYLHDEDMTFIAPDFVEDLAGKNGPEQQQATEHFMLALALCHTVV
AEKQPGDPPKMIFKAQSPDEAALVATARDMGFTVLGMSDGGINVNVMGKDMHFPVLSIIEFNSSRKRMSTIVRMPDGRIL
LFCKGADSVIYSRLKKGEQADMRRETAQHLEMFAVEGLRTLCIAERELSEEEYREWRREHDLAATALENREEKLEEVADK
IERDLTLLGGTAIEDRLQDGVPDTIALLADAGIKLWVLTGDKVETAINIGFSCNLLNNDMDLLRLQVNESDASTEDDYLQ
LAEEQLKTNLERFNMTGDDEELKRARKDHNAPSPTYALVIDGFTLRWVLSDSLKQKFLLLCKQCKSVLCCRVSPAQKAAV
VSMVKNGLDVMTLSIGDGANDVAMIQEADVGVGIAGEEGRQAVMSSDFAIGQFRFLQRLVLVHGRWSYRRLAETISNFFY
KNMIWTWSIFWYQCYCNFDIAYIFEYTYILMFNLFFTSVPVILMGVLDQDVSDTVSLAVPQLYRRGIERKEWTQTKFWLY
MIDGVYQSVMSFFIPFIFVVLTPTAAGNGLDVSERTRLGAYIAHPAVITINGYILINTYRWDWLMLLSIVLSDVFIFFWT
GVYTATTYSAGFYQAAPQVYQELTFWMCLIVTPALCLLPRLVVKCIQKQRFPYDVDIIREQANRGDFAAADAAAVAALGG
PERVEGESLGSLSSSGKGSGRSKKSKHQQYASVDEDRRPIYPPSIATHNTRAQNGSDGTTYIMQSRTSTELQQEMPFDRD
REEETPAVRPSIERTRPSYDRIRRSIDRVRPSFEASNDFTSAARLSRIESTHSSLGHTYSHQRESYAGESSGAQQGQEPG
QRRFNLATVRKRGLSAFSKKSIDTTEGEPPREPPM</string>
                    <external_references type="UNIPROTKB">G0S196</external_references>
                </sequence>
                <ec_number>7.6.2.1</ec_number>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Cdc50</name>
                <natural_source database="NCBI">
                    <organism ncbi="759272">Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)</organism>
                    <strain>DSM 1495 / CBS 144.50 / IMI 039719</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.046452311999999996</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MAPRRRRGAGQDGSDDGRSDSDAPKNRPPNTAFRQQRMRAWQCVLTPKLIVTVFSILAAIYLGFGAWLTYLAHTVRDLKI
DYTDCLTSAPKDDFETIPQNHITAHFSAKDSTFDPYKAQWKTTEREVQVANYTDNRQFCIVRFNIPEDLQPTISFFYYLE
NFYQNHRRYVNSFNAKQLLGDAVDGKTINDSTCDPITHDPKGTGKIVYPCGLVANSIFNDTFSSPLALAVRNSSDSSRPY
NMTTKGIAWPGLKDLYGKTSYSLDQIVPPPNWERRYKYGYQENNPPPDLKTDELFQNWMMLAAAPNFYKLYQKNDTHPML
AGQYEIEIESNFDVTVYKGRKAFVITTLSTMGSRNIWPGIIFLIVGGICLVLDIYFILSFFIWRPRKLGDPSYLSWNQPS
APGGHSS</string>
                    <external_references type="UNIPROTKB">G0SDN0</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="5">
                <name>MAGNESIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">2.4305e-05</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>MG</formula>
            </ligand>
            <ligand macromolecule_id="6">
                <name>PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000505208</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>ACP</formula>
            </ligand>
            <ligand macromolecule_id="7">
                <name>O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000792075</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>P5S</formula>
            </ligand>
            <ligand macromolecule_id="8">
                <name>2-acetamido-2-deoxy-beta-D-glucopyranose</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000221208</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>NAG</formula>
            </ligand>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">1.5</concentration>
                    <buffer>
                        <ph>7.5</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">297</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <average_electron_dose_per_image units="e/Å^2">57.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <particle_selection>
                    <number_selected>2397258</number_selected>
                </particle_selection>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <number_classes_used>2</number_classes_used>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.4</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <number_images_used>272912</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>8</number_classes>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="91626">
        <file>emd_0873.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>284</col>
            <row>284</row>
            <sec>284</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>284</x>
            <y>284</y>
            <z>284</z>
        </spacing>
        <cell>
            <a units="Å">299.62</a>
            <b units="Å">299.62</b>
            <c units="Å">299.62</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.1073686</minimum>
            <maximum>0.18286814</maximum>
            <average>0.00015012582</average>
            <std>0.0030677575</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.055</x>
            <y units="Å">1.055</y>
            <z units="Å">1.055</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.02</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0873::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
